public class TagSpectrumAnnotator extends SpectrumAnnotator
SpectrumAnnotator.TiesResolution
fragmentFactory, intensityLimit, ionMatchKeysCache, isPpm, massShift, massShiftCTerm, massShiftNTerm, maxIsotopicCorrection, minIsotopicCorrection, mzTolerance, precursorCharge, specificAnnotationSettings, subtractIsotope, theoreticalFragmentIons, tiesResolution
Constructor and Description |
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TagSpectrumAnnotator() |
Modifier and Type | Method and Description |
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ArrayList<IonMatch> |
getCurrentAnnotation(MSnSpectrum spectrum,
AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
boolean useIntensityFilter)
Returns the currently matched ions with the given settings.
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static NeutralLossesMap |
getDefaultLosses(Tag tag,
SequenceMatchingPreferences ptmSequenceMatchingSettings)
Returns the possible neutral losses expected by default for a given tag.
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ArrayList<IonMatch> |
getSpectrumAnnotation(AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
MSnSpectrum spectrum,
Tag tag)
Returns the spectrum annotations of a spectrum in a list of IonMatches using an intensity filter.
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ArrayList<IonMatch> |
getSpectrumAnnotation(AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
MSnSpectrum spectrum,
Tag tag,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
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Tag |
getTag()
Returns the tag to annotate.
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void |
setTag(Tag newTag,
int precursorCharge)
Sets a new tag to match.
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chargeValidated, getBestPeak, getCurrentAnnotation, getCurrentlyLoadedSpectrumKey, getDefaultLosses, getExpectedIons, getMassShift, getMassShiftCTerm, getMassShiftNTerm, getSpectrumAnnotation, isAccounted, lossesValidated, matchInSpectrum, matchPeak, matchReporterIon, setMassShift, setMassShifts, setMassTolerance, setSpectrum, setTerminalMassShifts, updateMassShifts
public Tag getTag()
public void setTag(Tag newTag, int precursorCharge)
newTag
- the new tagprecursorCharge
- the new precursor chargepublic static NeutralLossesMap getDefaultLosses(Tag tag, SequenceMatchingPreferences ptmSequenceMatchingSettings) throws IOException, InterruptedException, ClassNotFoundException
tag
- the tag of interestptmSequenceMatchingSettings
- the sequence matching settings for PTM
to peptide mappingIOException
- exception thrown whenever an error occurred while
interacting with a file while mapping potential modification sitesInterruptedException
- exception thrown whenever a threading issue
occurred while mapping potential modification sitesClassNotFoundException
- exception thrown whenever an error
occurred while deserializing an object from the ProteinTreepublic ArrayList<IonMatch> getSpectrumAnnotation(AnnotationSettings annotationSettings, SpecificAnnotationSettings specificAnnotationSettings, MSnSpectrum spectrum, Tag tag) throws InterruptedException, org.apache.commons.math.MathException
annotationSettings
- the annotation settingsspecificAnnotationSettings
- the specific annotation settingsspectrum
- the spectrum to matchtag
- the tag of interestInterruptedException
- exception thrown if a threading error occurred when estimating the noise levelorg.apache.commons.math.MathException
- exception thrown if a math exception occurred when estimating the noise levelpublic ArrayList<IonMatch> getSpectrumAnnotation(AnnotationSettings annotationSettings, SpecificAnnotationSettings specificAnnotationSettings, MSnSpectrum spectrum, Tag tag, boolean useIntensityFilter) throws InterruptedException, org.apache.commons.math.MathException
annotationSettings
- the annotation settingsspecificAnnotationSettings
- the specific annotation settingsspectrum
- the spectrum to matchtag
- the tag of interestuseIntensityFilter
- boolean indicating whether intensity filters should be usedInterruptedException
- exception thrown if a threading error occurred when estimating the noise levelorg.apache.commons.math.MathException
- exception thrown if a math exception occurred when estimating the noise levelpublic ArrayList<IonMatch> getCurrentAnnotation(MSnSpectrum spectrum, AnnotationSettings annotationSettings, SpecificAnnotationSettings specificAnnotationSettings, boolean useIntensityFilter) throws InterruptedException, org.apache.commons.math.MathException
SpectrumAnnotator
getCurrentAnnotation
in class SpectrumAnnotator
spectrum
- the spectrum of interestannotationSettings
- the annotation settingsspecificAnnotationSettings
- the specific annotation settingsuseIntensityFilter
- boolean indicating whether intensity filters should be usedInterruptedException
- exception thrown if a threading
error occurred when estimating the noise levelorg.apache.commons.math.MathException
- exception thrown if a math
exception occurred when estimating the noise levelCopyright © 2018. All rights reserved.